--- In a nutshell ---I lead a team of 16 people in charge of developing the tools serving contextual data and pathogeniticity prioritization to assist the clinicians in their decision making when analyzing variants detected in the patient.

A typical analysis performed at Sophia Genetics includes three steps:i) Targeting and sequencing the genomic regions of interest (primary analysis),ii) Detecting the variants using the best statistical approaches (secondary analysis)iii) Annotating the variants with as much relevant information to will help the medical geneticists in their decision process.--- In a nutshell ---I am responsible for developping and implementing the Tertiary analyses embarked in the Sophia Genetics pipelines. So far, I have designed and implemented the bioinformatics module assessing variants pathogenicity according to ACMG guidelines. This development was an important contribution to our latest major release (https://www.sophiagenetics.com/hospitals/sophia-ddm/know-more.html).

--- In a nutshell ---I manage a project based on:• 650,000 CHF funding delivered by the Swiss National Science Foundation and third parties. • My team includes a lab-technician, two master students.• We collaborate with scientists from Germany, United Kingdom, Netherlands and the United States of America.• We work within the department of Ecology and Evolution, at the University of Lausanne in Switzerland.--- Questions and approaches ---I address the evolutionary consequences of hybridization and selection. In practice, I aim at transferring an adaptation from one species into another by combining inter-specific crosses and artificial selection. I then track the genetic mechanisms at work, using next-generation sequencing, bioinformatics and modelling to address the following questions: • What are the genes at work behind the adaptation of interest?• Can we transfer them across species? • Do we observe varying rates of transfer among genes ? • How does that relate to genomic (e.g. chromosomal location) and functional constraints (e.g. role of the gene in the trait of interest; by discriminating effector from regulation genes) ?--- Scientific outcomes ---So far, we are at:• 10 peer-reviewed scientific publications accepted• 2 papers submitted• One bioinformatics pipeline detecting ancient genome duplications from transcriptome data (https://github.com/arrigon/WGDetect)• One simulator of introgression (R and C++), used for guiding our greenhouse experimental designOur experiments -using Brassicas- have reached the 4th generation of backcrosses (3 months, seed-to-seed) and we are not far from 20,000 progenies produced in total. We also have been actively sampling specimens from over 300 sites from natural populations and have started the DNA extractions.

--- In a nutshell ---I was in charge of the bioinformatics, data analysis and paper redaction within the group of Pr. Nadir Alvarez. --- Questions and approaches ---I worked on many population-genetics / phylogeography projects involving both plant and insects. We relied on :• MiSeq and HiSeq technologies (RAD-tags, environmental DNA, transcriptome and whole genome sequencing). • Bioinformatics and data analysis (using Perl, bash and R).--- Scientific outcomes ---• 9 peer-reviewed scientific publications.• Several bioinformatics pipelines (from raw reads to full assemblies).

--- In a nutshell ---I was in charge of :• 71,870 CHF funded by the Swiss National Science Foundation- at the University of Arizona (Tucson, USA).--- Questions and approaches ---I worked on those amazing resurrecting desert plants named Selaginella. Several of those have a hybrid origin and we went for sequencing their genomes and transcriptomes using the HiSeq and IonTorrent technologies.--- Scientific outcomes ---• 11 peer-reviewed scientific publications.• 6 genomes and 7 transcriptomes were produced.• One R package displaying datasets in Google Earth (https://cran.r-project.org/web/packages/R2G2/index.html)

Contribution to bioinformatic tools developed in the group of Pr. Nicolas Salamin.

Follow up on the PNR project "Hybridization between wheat and its wild relatives"- Experimental crosses involving wheat and its wild relatives.- Genotyping, (AFLP markers)- Statistical analyses, extensive usage of R (including development of libraries)